Thermo Fisher Scientific EASY-nLC Series Xcalibur Data System 2.1 or Later User guide

Thermo

EASY-nLC Series

User Guide for the Xcalibur Data System

Xcalibur 2.1 or later

60053-97230 Revision C November 2013

EASY-nLC, EASY-Column, AFC, Foundation, IFC, and LTQ XL are trademarks, and Xcalibur and LTQ are

registered trademarks of Thermo Fisher Scientific Inc.

The following are registered trademarks in the United States and other countries: Microsoft and Windows are

registered trademarks of the Microsoft Corporation. McAfee and VirusScan are registered trademarks of

McAfee, Inc.

All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the

product operation. This document is copyright protected and any reproduction of the whole or any part of this

document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-

free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might

result from any use of this document, even if the information in the document is followed properly.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This

document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of

Sale shall govern all conflicting information between the two documents.

Release history: Revision A, July 2012; Revision B, January 2013; Revision C, November 2013

Software version: Foundation platform version 1.0.2 SP2 or later, Xcalibur data system version 2.1 or later

(installed on the Foundation platform), EASY-nLC device driver version 2.7 or later

For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System iii

C

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Data System Computer Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

Chapter 1 Installing the EASY-nLC Control Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Checking the System Prerequisites. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Removing a Previous Version of the Instrument Control Software . . . . . . . . . . . 2

Installing the Current Version of the Instrument Control Software. . . . . . . . . . . 4

Excluding the EASY-nLC from the VirusScan Enterprise . . . . . . . . . . . . . . . . . . 5

Chapter 2 Setting Up the Foundation Instrument Configuration. . . . . . . . . . . . . . . . . . . . . . . .7

Connecting the EASY-nLC Instrument to the Data System Computer . . . . . . . . 7

Adding the System Devices to the Instrument Configuration . . . . . . . . . . . . . . . 8

Setting Up the EASY-nLC Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Setting Up the Sample Layout and Start Position . . . . . . . . . . . . . . . . . . . . . . . 17

Chapter 3 Creating Xcalibur Instrument Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Setting Up the EASY-nLC Instrument Method Parameters. . . . . . . . . . . . . . . . 21

Sample Pickup and Loading Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Gradient Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Pre-Column and Analytical Column Page . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Auto-Sampler Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Saving Instrument Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Chapter 4 Creating and Running Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35

Creating Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Setting Up the Injection Positions with the Sample Position Selector . . . . . . . . 41

Running Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Taking Corrective Action for Run-Time Errors. . . . . . . . . . . . . . . . . . . . . . . . . 45

Contents

iv EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Chapter 5 Viewing the Run Status in the Information View . . . . . . . . . . . . . . . . . . . . . . . . . .47

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System v

P

Preface

This guide describes how to configure the Thermo EASY-nLC™ virtual instrument (VI)

control software from the Thermo Foundation™ platform, set up the liquid chromatography

(LC) parameters for LC/MS instrument methods in the Instrument Setup window of the

Thermo Xcalibur™ data system, and set up the sample position settings and injection volumes

for an injection sequence from the Sequence Setup view in the Xcalibur data system.

To suggest changes to the documentation or to the Help

Complete a brief survey about this document by clicking the button below.

Thank you in advance for your help.

IMPORTANT To establish communication with the EASY-nLC instrument and to

avoid the premature termination of data acquisition during sequence runs, set up the data

system computer as described in “Data System Computer Settings” on page viii.

Contents

•Related Documentation

•System Requirements

•Data System Computer Settings

•Cautions and Special Notices

•Contacting Us

Preface

vi EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Related Documentation

Thermo Fisher Scientific provides these manuals as PDF files on the data system computer

and on the USB flash drive that ships with the EASY-nLC instrument:

• EASY-nLC Series Preinstallation Requirements Guide

•EASY-nLC Series Getting Started Guide (using the stand-alone, touch-screen application)

• EASY-nLC Series Troubleshooting and Maintenance Guide

• EASY-nLC Series User Guide for the Xcalibur Data System

The data system also provides Help for the EASY-nLC virtual instrument control software.

To access the EASY-nLC manuals on the data system computer

Choose Start > Programs (or All Programs) > Thermo Instruments > Manuals >

LC Devices > Thermo.

To open the Help from the EASY-nLC view of the Instrument Setup window

• To open the Welcome page of the Thermo EASY-nLC Help, choose Help > Thermo

EASY-nLC Help from the menu bar.

• To open the Help topic for the current page of the Thermo EASY-nLC view, do one

of the following:

– Choose Help > Help On Current Item F1 from the menu bar.

– Press the F1 key on the computer keyboard.

To open the Help from the Thermo EASY-nLC Configuration dialog box of the

Foundation Instrument Configuration window

Press the F1 key on the computer keyboard.

Preface

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System vii

System Requirements

Tabl e 1 lists the data system computer hardware and software requirements for the EASY-nLC

device driver. This device driver is provided on the LC Devices DVD and is designed for use

with the Thermo Xcalibur data system or an equivalent Thermo Scientific mass spectrometry

application.

IMPORTANT Before you install the device driver provided on the LC Devices DVD,

ensure that the data system computer has a compatible version of the Foundation

platform as noted in the Thermo LC Devices x.x.x Release Notes, where x.x.x is the version

you want to install. You can find the Release Notes document, which includes the system

requirements, on the LC Devices DVD.

Table 1. Data system computer hardware and software requirements

Hardware Minimum requirements

Data system computer • 2 GHz processor with 1 GB RAM

• DVD-ROM drive

• 80 GB hard drive capacity

• Display resolution 1280 × 1024 resolution

• 2 Network cards

•NTFS format

Software Requirements

Operating system Microsoft™ Windows™ operating system:

• Windows 7 Professional (32-bit and 64-bita)

–or–

• Windows XP Workstation SP3

aLC Devices 2.8.0 and later are compatible with Windows 7, 32-bit and 64-bit

Third-party software Adobe™ Reader™ 9.0 or later

Thermo Scientific software LC Devices

EASY-nLC device driver

Foundation platform

2.8.0 or later 1.0.2 SP2 or later

2.7.0 1.0.2 SP2 or 2.0.0 SP1

Preface

viii EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Data System Computer Settings

Tabl e 2 lists the computer settings that are required to avoid the premature termination of

data acquisition during sequence runs. It also provides the virus scanner setting that is

required to establish communication with the EASY-nLC instrument.

IMPORTANT After you install the Thermo EASY-nLC device driver on a Windows 7

computer, exclude the Thermo EASY-nLC software from the Prevent IRC

Communication list for the computer’s virus scanner (see “Excluding the EASY-nLC from

the VirusScan Enterprise” on page 5).

If you do not exclude the Thermo EASY-nLC software from the Prevent IRC

Communication list, the data system computer cannot establish communication with the

EASY-nLC instrument.

Table 2. Data system computer settings

Category Settings

Power saver • Screen saver: None

• Hibernate: Not enabled or Never

• Turn off hard disk: Never

• Turn off monitor: Never

Windows updates If the data system computer is connected to the Internet, turn

off the automatic Windows updates.

Virus scanner For the Windows 7 operating system, exclude the

Thermo EASY-nLC software from the virus scanner.

Preface

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System ix

Cautions and Special Notices

Make sure you follow the cautions and special notices presented in this guide. Cautions and

special notices appear in boxes; those concerning safety or possible system damage also have

corresponding caution symbols.

This guide uses the following types of cautions and special notices.

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION

notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal

performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Preface

xEASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Contacting Us

There are several ways to contact Thermo Fisher Scientific for the information you need.

To contact Technical Support for the EASY-nLC instrument

Find software updates and utilities to download at mssupport.thermo.com.

To order consumable and spare parts for the EASY-nLC instrument

For the EASY-nLC 1000 instrument, go to

www.proxeon.com/productrange/nano_lc_easy-nlc_1000/accessories_spares/index.html.

For the EASY-nLC II instrument, go to

www.proxeon.com/productrange/nano_lc/accessories-spares/index.html.

To get local contact information for sales or service

Go to www.thermoscientific.com/wps/portal/ts/contactus.

To copy manuals from the Internet

Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click

Customer Manuals in the left margin of the window.

To suggest changes to the documentation or to the Help

• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.

• Send an e-mail message to the Technical Publications Editor at

techpubs-lcms@thermofisher.com.

Phone 800-532-4752

Fax 561-688-8736

Web site www.proxeon.com

E-mail (North and South America)

us.techsupport.analyze@thermofisher.com

(Other continents)

eu.techsupport.cmf@thermofisher.com

Knowledge base www.thermokb.com

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System 1

1

Installing the EASY-nLC Control Software

This chapter describes how to install the EASY-nLC virtual instrument (VI) control software

from the LC Devices DVD. It also describes how to ensure communication between the data

system computer and the EASY-nLC instrument.

Checking the System Prerequisites

The LC/MS system consists of the EASY-nLC instrument, a Thermo Scientific mass

spectrometer, and a data system computer.

Before installing the EASY-nLC VI control software, do the following:

• Install compatible versions of the Thermo Foundation platform and the Xcalibur data

system (or equivalent Thermo Scientific data system).

• Ensure that you have administrator rights to install the EASY-nLC VI control software

for the Xcalibur application.

• Remove any earlier version of the EASY-nLC VI control software from the data system

computer (see “Removing a Previous Version of the Instrument Control Software” on

page 2).

Contents

•Checking the System Prerequisites

•Removing a Previous Version of the Instrument Control Software

•Installing the Current Version of the Instrument Control Software

•Excluding the EASY-nLC from the VirusScan Enterprise

1 Installing the EASY-nLC Control Software

Removing a Previous Version of the Instrument Control Software

2EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Before or after installing the EASY-nLC VI control software, do the following:

• Connect the EASY-nLC instrument to the data system computer through an Ethernet

connection (see “Connecting the EASY-nLC Instrument to the Data System Computer”

on page 7).

• Connect the EASY-nLC instrument to the Thermo Scientific MS detector with a contact

closure cable.

The data system synchronizes the run timing between the LC system and the mass

spectrometer through the cable. For information about connecting the contact closure

cable, refer to the EASY-nLC Series Getting Started Guide.

• Check the laboratory local area network (LAN) port for Internet access to the remote

support server. For remote diagnostics, the laboratory must have a LAN port with

Internet access.

The network firewall must allow outgoing Transmission Control Protocol/Internet

Protocol (TCP/IP) traffic from the EASY-nLC instrument to the remote support server at

IP address 195.41.108.93, port 22.

After installing the EASY-nLC VI control software, exclude the software from the virus

scanner as described in “Excluding the EASY-nLC from the VirusScan Enterprise” on page 5.

Removing a Previous Version of the Instrument Control Software

To remove a previously installed version of the EASY-nLC Xcalibur VI

1. Depending on the Windows operating system, do one of the following:

• For Windows 7, choose Control Panel > Uninstall a Program.

The list of installed programs appears (see Figure 1).

• For Windows XP, choose Start > Settings > Control Panel > Add or Remove

Programs.

1 Installing the EASY-nLC Control Software

Removing a Previous Version of the Instrument Control Software

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System 3

Figure 1. Uninstall window for the Windows 7 operating system

2. In the list of installed programs, locate Thermo LC Devices Thermo EASY-nLC

Xcalibur VI.

3. Depending on the operating system, do one of the following:

• For Windows 7, double-click Thermo LC Devices Thermo EASY-nLC Xcalibur VI

or click Uninstall. Wait for the program to be removed from the list.

• For Windows XP, click Remove (see Figure 2). Wait for the program to be removed

from the list.

Figure 2. Add or Remove Programs window for the Windows XP operating system

1 Installing the EASY-nLC Control Software

Installing the Current Version of the Instrument Control Software

4EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Installing the Current Version of the Instrument Control Software

To install the EASY-nLC Virtual Instrument software

1. Check the installed versions of the Foundation platform and the Xcalibur data system and

make sure that these versions are compatible with the LC Devices version that you are

installing (see “System Requirements” on page vii).

2. Close all running programs before starting the installation.

3. If applicable, remove the previously installed version of the EASY-nLC VI software

(see “Removing a Previous Version of the Instrument Control Software” on page 2).

4. Load the LC Devices DVD into the data system computer, and follow the instructions in

the Thermo LC Devices InstallShield Wizard.

5. On the Select Features page of the wizard, select the Thermo check box on the left, and

then select the Thermo EASY-nLC Xcalibur check box on the right (see Figure 3).

Figure 3. Select Features page of the Thermo LC Devices InstallShield Wizard

6. When the installation finishes, restart the data system computer.

The installation is complete when you log back in.

1 Installing the EASY-nLC Control Software

Excluding the EASY-nLC from the VirusScan Enterprise

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System 5

Excluding the EASY-nLC from the VirusScan Enterprise

The McAfee™ VirusScan™ Enterprise software blocks the Thermo EASY-nLC software when

the data system computer uses the Windows 7 operating system.

To exclude the EASY-nLC software from the VirusScan Enterprise 8.7.0i software

1. Log in to the data system computer as an administrator.

2. Open the McAfee VirusScan Console application as follows:

a. Do one of the following:

• On the Windows 7 taskbar, right-click the McAfee icon, , and choose

Manage Features > VirusScan Enterprise.

–or–

• From the Windows 7 desktop, choose Start > All Programs > McAfee >

VirusScan Console.

3. In the Task column, right-click Access Protection and choose Properties from the

shortcut menu.

The Access Protection Properties dialog box appears.

4. To open the Rules dialog box, do the following:

a. Under Categories, choose Anti-virus Standard Protection.

b. Under Rules, select Prevent IRC Communication.

c. Click Edit.

The Rules Details dialog box opens.

5. Modify these settings:

• In the Processes to Include box, delete the asterisk.

• In the Processes to Exclude box, type Thermo*.

IMPORTANT For the Windows 7 operating system, you must exclude the EASY-nLC

VI software from the McAfee blocking list. For the Windows XP operating system,

exclude the EASY-nLC VI software from the McAfee blocking list only if the EASY-nLC

instrument is experiencing communication problems.

Note When the Processes to Include box contains only a single asterisk, the virus

scanner prevents IRC communication for all processes.

Note When the Processes to Exclude box contains the text Thermo*, the Access

Protection service for Internet Relay Chat (IRC) communication processes

ignores processes that begin with Thermo.

1 Installing the EASY-nLC Control Software

Excluding the EASY-nLC from the VirusScan Enterprise

6EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

6. Click OK to close the Rules Details dialog box.

7. Click OK to close the Access Protection Properties dialog box and accept the new

settings.

8. Close the VirusScan Console application.

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System 7

2

Setting Up the Foundation Instrument Configuration

This chapter describes how to set up the instrument configuration for the EASY-nLC device

driver.

Before you set up the instrument configuration, connect the EASY-nLC instrument to the

data system computer, turn on the EASY-nLC instrument, and log in to the instrument as an

administrator. Then, use the Thermo EASY-nLC Configuration dialog box of the Thermo

Foundation Instrument Configuration window to set up and test the network connection for

the EASY-nLC instrument, to specify the tray type that you plan to use, and to identify the

mobile phase solvents in solvent reservoir bottles A and B.

Connecting the EASY-nLC Instrument to the Data System Computer

The EASY-nLC instrument and the Thermo Scientific mass spectrometer communicate with

the data system computer through an Ethernet connection routed through an Ethernet switch

connected to the data system computer.

These are the default IP addresses of the data system computer and the EASY-nLC

instrument.

Contents

•Connecting the EASY-nLC Instrument to the Data System Computer

•Adding the System Devices to the Instrument Configuration

•Setting Up the EASY-nLC Configuration

•Setting Up the Sample Layout and Start Position

Table 3. Default IP addresses for the LC system

System module IP address

Data system computer 172.16.0.101

EASY-nLC instrument 172.16.0.103

2 Setting Up the Foundation Instrument Configuration

Adding the System Devices to the Instrument Configuration

8EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

To connect the EASY-nLC instrument to the data system computer

1. Connect a shielded Ethernet cable to the LAN port on the back panel of the EASY-nLC

instrument.

2. Connect the other end of the Ethernet cable to an Ethernet switch.

3. Using a second shielded Ethernet cable, connect the Ethernet switch to the appropriate

network card installed in the data system computer.

For more information about setting up the communication cables, refer to the EASY-nLC

Series Getting Started Guide.

Adding the System Devices to the Instrument Configuration

Your Thermo Scientific LC/MS system consists of a Thermo Scientific mass spectrometer and

an EASY-nLC instrument. To control these instruments from the Xcalibur data system, you

must add the installed device drivers to the instrument configuration.

To add devices to the instrument configuration

1. Close the Xcalibur data system if it is open.

2. From the Windows taskbar, choose Start > Programs (or All Programs) >

Thermo Foundation x.x > Instrument Configuration, where x.x is the installed version

of Thermo Foundation.

The Thermo Foundation Instrument Configuration window opens (see Figure 4). The

installed devices are listed in the Available Devices list. The configured devices are listed

in the Configured Devices list.

Figure 4 shows an instrument configuration with a Thermo Scientific mass spectrometer

added to the Configured Devices list.

IMPORTANT Avoid IP conflicts with other units on the network, especially the

mass spectrometer.

Note The Xcalibur data system and the Foundation Instrument Configuration window

cannot be open simultaneously.

2 Setting Up the Foundation Instrument Configuration

Adding the System Devices to the Instrument Configuration

Thermo Scientific EASY-nLC Series User Guide for the Xcalibur Data System 9

Figure 4. Thermo Foundation Instrument Configuration window

3. Add the EASY-nLC instrument to the instrument configuration as follows:

a. Make sure that the Device Types list is set to All or AS (Autosampler).

If the Device Type list is set to LC, the EASY-nLC VI for Xcalibur device does not

appear in the Available Devices list.

b. In the Available Devices list, double-click the Thermo EASY-nLC icon.

A copy of the Thermo EASY-nLC icon appears in the Configured Devices list.

4. Set up the configuration options for each configured device.

For information about the EASY-nLC configuration parameters, see the next topic,

“Setting Up the EASY-nLC Configuration.”

5. Click Done to close the Thermo Foundation Instrument Configuration window.

Tip To access Help, press F1 or click Help.

Tip You must close the Instrument Configuration window before you open the

Xcalibur data system. The two applications cannot be open at the same time.

2 Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration

10 EASY-nLC Series User Guide for the Xcalibur Data System Thermo Scientific

Setting Up the EASY-nLC Configuration

Use the Thermo EASY-nLC Configuration dialog box to set up and test the communication

connection to the data system computer, to specify the autosampler model and the plate type

that you are using, and to identify the mobile phase solvents. Clicking the Edit button in the

Autosampler Configuration area opens the Sample Position Selector dialog box where you set

up the sample layout (row first or column first) and the start position for an Xcalibur injection

sequence.

To set up the EASY-nLC configuration in the Foundation platform

1. If you have not already added the EASY-nLC instrument to the Configured Devices list

of the Thermo Foundation Instrument Configuration window, add it as described in

“Adding the System Devices to the Instrument Configuration” on page 8.

2. In the Configured Devices list of the Thermo Foundation Instrument Configuration

window, double-click the Thermo EASY-nLC icon.

The Thermo EASY-nLC Configuration dialog box opens (see Figure 5).

Figure 5. Thermo EASY-nLC Configuration dialog box

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Thermo Fisher Scientific EASY-nLC Series Xcalibur Data System 2.1 or Later User guide

Thermo Fisher Scientific EASY-nLC Series Xcalibur Data System 2.1 or Later User guide

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